vorontsovie / bioinform Goto Github PK

Hello Ilya,

This may be really minor but I had a look at files such a validator.rb

There is code such as this:

def to_s
      msg = ""

      if errors && !errors.empty?
        msg += "Errors:\n" + errors.join("\n") + "\n"
      end

      if warnings && !warnings.empty?
        msg += "Warnings:\n" + warnings.join("\n")
      end

      msg.empty? ? "{No errors, no warnings}" : "{#{msg}}"
    end

You can replace "msg +=" with "msg <<".

The reason why I mention this is because << is slightly faster than +=
because you avoid creating a new string object via <<, whereas the
+= variant will create a new String object.

You can try this in IRB to see the new string ID:

x = 'abc'       # => "abc"
x.object_id     # => 76410130
x += 'def'      # => "abcdef"
x.object_id     # => 76379190

x = 'abc'       # => "abc"
x.object_id     # => 76332000
x << 'def'      # => "abcdef"
x.object_id     # => 76332000

You can see in the second example via << the object id
stays the same; in the first example it is changed.

Thanks for reading! May the elegance of ruby be with you.

Hello Ilya,

I had a look at your bioinform gem. You have a README.md in where you list "Command-line applications".

In particular:

• pcm2pwm
• split_motifs
• merge_into_collection

Could you perhaps consider adding ONE usage example for each? Just a short line, e. g. how to use it with any dataset. I would like to test the bioinform gem but I struggle a bit with how things fit together, how to use them and so on.

Thank you for reading! May the beauty of ruby be with you.